Merge BRIDGE into main in prep for release v17.9.5 (#448)

- Zero-diff vs. v17.9.3 for model-only simulations without perturbations using a build with standard optimization.

- Not zero-diff for simulations with perturbations (including data assimilation) or any simulation using a build with aggressive optimization.

- Science changes:
  - Added S2S/AODAS and S2S/Forecast surface met forcing reader.

- Infrastructure:
  - Parallel FFT on each node using shared memory (non-zero-diff change for perturbations and data assimilation).
  - Refined assignment of tiles to processors (non-zero-diff change with aggressive optimization).
  - By default, limit MKL's freedom to choose algorithms during runtime (MKL_CBWR=AVX2), to ensure 0-diff across architectures.
  - Updated ESMA_env (v3.3.0) --> Baselibs (6.2.4), ESMA_cmake (v3.5.0).
  - Updated GMAO_Shared (v1.4.4).
  - Updated GEOSgcm_GridComp (v1.12.3).

- Documentation:
  - Clarified help text for RESTART option in ldas_setup.

- Bug fixes and other minor changes:
  - Minor fixes to support debugging and non-Intel compilers (GNU).

.circleci/config.yml

@@ -1,9 +1,9 @@
 version: 2.1
 
 executors:
-  gcc-build-env:
+  gfortran-large:
     docker:
-      - image: gmao/ubuntu20-geos-env-mkl:v6.2.4-openmpi_4.0.5-gcc_10.3.0
+      - image: gmao/ubuntu20-geos-env-mkl:v6.2.7-openmpi_4.0.6-gcc_11.2.0
         auth:
           username: $DOCKERHUB_USER
           password: $DOCKERHUB_AUTH_TOKEN
@@ -14,24 +14,39 @@ executors:
     resource_class: large
     #MEDIUM# resource_class: medium
 
+  ifort-large:
+    docker:
+      - image: gmao/ubuntu20-geos-env:v6.2.7-intelmpi_2021.2.0-intel_2021.2.0
+        auth:
+          username: $DOCKERHUB_USER
+          password: $DOCKERHUB_AUTH_TOKEN
+    resource_class: large
+    #MEDIUM# resource_class: medium
+
 workflows:
-  version: 2.1
   build-test:
     jobs:
       - build-GEOSldas:
+          name: build-GEOSldas-on-<< matrix.compiler >>
+          matrix:
+            parameters:
+              compiler: [gfortran, ifort]
           context:
             - docker-hub-creds
 
 jobs:
   build-GEOSldas:
-    executor: gcc-build-env
+    parameters:
+      compiler:
+        type: string
+    executor: << parameters.compiler >>-large
     working_directory: /root/project
     steps:
       - checkout:
           path: GEOSldas
       - run:
           name: "Versions etc"
-          command: mpirun --version && gfortran --version && echo $BASEDIR && pwd && ls
+          command: mpirun --version && << parameters.compiler>> --version && echo $BASEDIR && pwd && ls
       - run:
           name: "Mepo clone external repos"
           command: |
@@ -51,13 +66,16 @@ jobs:
       - run:
           name: "CMake"
           command: |
+            mkdir -p /logfiles
             cd ${CIRCLE_WORKING_DIRECTORY}/GEOSldas
-            mkdir build
-            cd build
-            cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug -DUSE_F2PY=OFF
+            mkdir -p  ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSldas
+            cd ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSldas
+            cmake ${CIRCLE_WORKING_DIRECTORY}/GEOSldas -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=<< parameters.compiler >> -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=${CIRCLE_WORKING_DIRECTORY}/workspace/install-GEOSldas -DUSE_F2PY=OFF |& tee /logfiles/cmake.log
       - run:
-          name: "Build"
+          name: "Build and install"
           command: |
-            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSldas/build
-            make -j"$(nproc)" install
-            #MEDIUM# make -j4 install
+            cd ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSldas
+            make -j"$(nproc)" install |& tee /logfiles/make.log
+            #MEDIUM# make -j4 install |& tee /logfiles/make.log
+      - store_artifacts:
+          path: /logfiles

CMakeLists.txt

@@ -18,7 +18,7 @@ if (NOT CMAKE_BUILD_TYPE)
   set (CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
   # Set the possible values of build type for cmake-gui
   set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
-    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+    "Debug" "Release" "Aggressive")
 endif ()
 
 set (DOING_GEOS5 YES)
@@ -53,4 +53,5 @@ install(
    DESTINATION ${CMAKE_INSTALL_PREFIX}
    )
 
-
+# Adds abiilty to tar source
+include (esma_cpack)

LICENSE.md

@@ -1,7 +1,9 @@
 ```
-Copyright (c) 2003-2018 United States Government as represented by 
-the Admistrator of the National Aeronautics and Space Administration.  
-All Rights Reserved.
+
+    	NASA OPEN SOURCE SOFTWARE AGREEMENT
+	
+
+NASA OPEN SOURCE AGREEMENT VERSION 1.3
 
 THIS OPEN  SOURCE  AGREEMENT  ("AGREEMENT") DEFINES  THE  RIGHTS  OF USE,
 REPRODUCTION,  DISTRIBUTION,  MODIFICATION AND REDISTRIBUTION OF CERTAIN 
@@ -19,5 +21,243 @@ Government Agency Original Software Designation: GSC-15354-1
 Government Agency Original Software Title:  GEOS-5 GCM Modeling Software
 User Registration Requested.  Please Visit http://opensource.gsfc.nasa.gov
 Government Agency Point of Contact for Original Software:  
-			Dale Hithon, SRA Assistant, (301) 286-2691
+            Dale Hithon, SRA Assistant, (301) 286-2691
+
+1. DEFINITIONS
+
+A.  "Contributor" means Government Agency, as the developer of the
+Original Software, and any entity that makes a Modification.
+
+B.  "Covered Patents" mean patent claims licensable by a Contributor
+that are necessarily infringed by the use or sale of its Modification
+alone or when combined with the Subject Software.
+
+C.  "Display" means the showing of a copy of the Subject Software,
+either directly or by means of an image, or any other device.
+
+D.  "Distribution" means conveyance or transfer of the Subject Software,
+regardless of means, to another.
+
+E.  "Larger Work" means computer software that combines Subject
+Software, or portions thereof, with software separate from the Subject
+Software that is not governed by the terms of this Agreement.
+
+F.  "Modification" means any alteration of, including addition to
+or deletion from, the substance or structure of either the Original
+Software or Subject Software, and includes derivative works, as that
+term is defined in the Copyright Statute, 17 USC 101.  However, the act
+of including Subject Software as part of a Larger Work does not in and
+of itself constitute a Modification.
+
+G.  "Original Software" means the computer software first released under
+this Agreement by Government Agency with Government Agency designation
+GSC-15354-1 and entitled GEOS-5 GCM Modeling Software, including source
+code, object code and accompanying documentation, if any.
+
+H.  "Recipient" means anyone who acquires the Subject Software under
+this Agreement, including all Contributors.
+
+I.  "Redistribution" means Distribution of the Subject Software after a
+Modification has been made.
+
+J.  "Reproduction" means the making of a counterpart, image or copy of
+the Subject Software.
+
+K.  "Sale" means the exchange of the Subject Software for money or
+equivalent value.
+
+L.  "Subject Software" means the Original Software, Modifications, or
+any respective parts thereof.
+
+M.  "Use" means the application or employment of the Subject Software
+for any purpose.
+
+
+
+2. GRANT OF RIGHTS
+
+A.  Under Non-Patent Rights: Subject to the terms and conditions of this
+Agreement, each Contributor, with respect to its own contribution to
+the Subject Software, hereby grants to each Recipient a non-exclusive,
+world-wide, royalty-free license to engage in the following activities
+pertaining to the Subject Software:
+
+1. Use
+2. Distribution
+3. Reproduction
+4. Modification 
+5. Redistribution
+6. Display
+
+B.  Under Patent Rights: Subject to the terms and conditions of this
+Agreement, each Contributor, with respect to its own contribution to
+the Subject Software, hereby grants to each Recipient under Covered
+Patents a non-exclusive, world-wide, royalty-free license to engage in
+the following activities pertaining to the Subject Software:
+
+1. Use
+2. Distribution
+3. Reproduction
+4. Sale
+5. Offer for Sale
+
+C.  The rights granted under Paragraph B. also apply to the combination
+of a Contributor's Modification and the Subject Software if, at the
+time the Modification is added by the Contributor, the addition of
+such Modification causes the combination to be covered by the Covered
+Patents.  It does not apply to any other combinations that include a
+Modification.
+
+D.  The rights granted in Paragraphs A. and B. allow the Recipient to
+sublicense those same rights.  Such sublicense must be under the same
+terms and conditions of this Agreement.
+
+
+3. OBLIGATIONS OF RECIPIENT
+
+A.  Distribution or Redistribution of the Subject Software must be made
+under this Agreement except for additions covered under paragraph 3H.
+
+1.  Whenever a Recipient distributes or redistributes the Subject
+Software, a copy of this Agreement must be included with each copy of
+the Subject Software; and
+
+2.  If Recipient distributes or redistributes the Subject Software in
+any form other than source code, Recipient must also make the source
+code freely available, and must provide with each copy of the Subject
+Software information on how to obtain the source code in a reasonable
+manner on or through a medium customarily used for software exchange.
+
+B.  Each Recipient must ensure that the following copyright notice
+appears prominently in the Subject Software:
+
+Copyright © 2003-2018 United States Government as represented by the
+Administrator of the National Aeronautics and Space Administration.  All
+Rights Reserved.
+
+C.  Each Contributor must characterize its alteration of the Subject
+Software as a Modification and must identify itself as the originator
+of its Modification in a manner that reasonably allows subsequent
+Recipients to identify the originator of the Modification.  In
+fulfillment of these requirements, Contributor must include a file
+(e.g., a change log file) that describes the alterations made and
+the date of the alterations, identifies Contributor as originator of
+the alterations, and consents to characterization of the alterations
+as a Modification, for example, by including a statement that the
+Modification is derived, directly or indirectly, from Original Software
+provided by Government Agency. Once consent is granted, it may not
+thereafter be revoked.
+
+D.  A Contributor may add its own copyright notice to the Subject
+Software.  Once a copyright notice has been added to the Subject
+Software, a Recipient may not remove it without the express permission
+of the Contributor who added the notice.
+
+E.  A Recipient may not make any representation in the Subject Software
+or in any promotional, advertising or other material that may be
+construed as an endorsement by Government Agency or by any prior
+Recipient of any product or service provided by Recipient, or that may
+seek to obtain commercial advantage by the fact of Government Agency's
+or a prior Recipient's participation in this Agreement.
+
+F.  In an effort to track usage and maintain accurate records of
+the Subject Software, each Recipient, upon receipt of the Subject
+Software, is requested to register with Government Agency by visiting
+the following website: http://opensource.gsfc.nasa.gov.  Recipient's
+name and personal information shall be used for statistical purposes
+only. Once a Recipient makes a Modification available, it is requested
+that the Recipient inform Government Agency at the web site provided
+above how to access the Modification.
+
+G.  Each Contributor represents that its Modification is believed to
+be Contributor's original creation and does not violate any existing
+agreements, regulations, statutes or rules, and further that Contributor
+has sufficient rights to grant the rights conveyed by this Agreement.
+
+H.  A Recipient may choose to offer, and to charge a fee for, warranty,
+support, indemnity and/or liability obligations to one or more other
+Recipients of the Subject Software.  A Recipient may do so, however,
+only on its own behalf and not on behalf of Government Agency or any
+other Recipient.  Such a Recipient must make it absolutely clear that
+any such warranty, support, indemnity and/or liability obligation is
+offered by that Recipient alone.  Further, such Recipient agrees to
+indemnify Government Agency and every other Recipient for any liability
+incurred by them as a result of warranty, support, indemnity and/or
+liability offered by such Recipient.
+
+I.  A Recipient may create a Larger Work by combining Subject Software
+with separate software not governed by the terms of this agreement
+and distribute the Larger Work as a single product. In such case, the
+Recipient must make sure Subject Software, or portions thereof, included
+in the Larger Work is subject to this Agreement.
+
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+put on notice that export of any goods or technical data from the United
+States may require some form of export license from the U.S. Government.
+Failure to obtain necessary export licenses may result in criminal
+liability under U.S. laws.  Government Agency neither represents that a
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+Nothing granted herein provides any such export license.
+
+4. DISCLAIMER OF WARRANTIES AND LIABILITIES; WAIVER AND INDEMNIFICATION
+
+A. No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT
+ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY,
+INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT
+SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM
+INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR FREE,
+OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE
+SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN
+ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT OF ANY RESULTS,
+RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER APPLICATIONS
+RESULTING FROM USE OF THE SUBJECT SOFTWARE. FURTHER, GOVERNMENT AGENCY
+DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE,
+IF PRESENT IN THE ORIGINAL SOFTWARE, AND DISTRIBUTES IT "AS IS."
+
+B. Waiver and Indemnity: RECIPIENT AGREES TO WAIVE ANY AND ALL
+CLAIMS AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND
+SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT.  IF RECIPIENT'S USE
+OF THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES,
+EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM
+PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT
+SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED STATES
+GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR
+RECIPIENT, TO THE EXTENT PERMITTED BY LAW.  RECIPIENT'S SOLE REMEDY FOR
+ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL TERMINATION OF THIS
+AGREEMENT.
+
+5. GENERAL TERMS
+
+A.  Termination: This Agreement and the rights granted hereunder will
+terminate automatically if a Recipient fails to comply with these terms
+and conditions, and fails to cure such noncompliance within thirty
+(30) days of becoming aware of such noncompliance.  Upon termination,
+a Recipient agrees to immediately cease use and distribution of the
+Subject Software.  All sublicenses to the Subject Software properly
+granted by the breaching Recipient shall survive any such termination of
+this Agreement.
+
+B.  Severability: If any provision of this Agreement is invalid or
+unenforceable under applicable law, it shall not affect the validity or
+enforceability of the remainder of the terms of this Agreement.
+
+C.  Applicable Law: This Agreement shall be subject to United States
+federal law only for all purposes, including, but not limited to,
+determining the validity of this Agreement, the meaning of its
+provisions and the rights, obligations and remedies of the parties.
+
+D.  Entire Understanding: This Agreement constitutes the entire
+understanding and agreement of the parties relating to release of the
+Subject Software and may not be superseded, modified or amended except
+by further written agreement duly executed by the parties.
+
+E. Binding Authority: By accepting and using the Subject Software under
+this Agreement, a Recipient affirms its authority to bind the Recipient
+to all terms and conditions of this Agreement and that that Recipient
+hereby agrees to all terms and conditions herein.
+
+F. Point of Contact: Any Recipient contact with Government Agency is to
+be directed to the designated representative as follows:  Dale Hithon,
+SRA Assistant, (301) 286-2691.
 ```

components.yaml

@@ -9,7 +9,7 @@ env:
 cmake:
   local: ./@cmake
   remote: ../ESMA_cmake.git
-  tag: v3.5.0
+  tag: v3.5.5
 
 ecbuild:
   local: ./@cmake/@ecbuild
@@ -20,15 +20,15 @@ GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
   sparse: ./config/GMAO_Shared.sparse
-  tag: v1.4.4
+  tag: v1.4.6
 
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.7.0
+  tag: v2.8.6
 
 GEOSgcm_GridComp:
   local: ./src/Components/GEOSldas_GridComp/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
   sparse: ./config/GEOSgcm_GridComp_ldas.sparse
-  tag: v1.12.3
+  tag: v1.12.4